Use of artificial neural network for pretreatment verification of intensity modulation radiation therapy fields.

OBJECTIVE: The accuracy of dose delivery for intensity modulated radiotherapy (IMRT) treatments should be determined by an accurate quality assurance procedure. In this work, we used artificial neural networks (ANNs) as an application for the pre-treatment dose verification of IMRT fields based two-dimensional-fluence maps acquired by an electronic portal imaging device (EPID). METHODS: The ANN must be trained and validated before use for the pretreatment dose verification. Hence, 60 EPID fluence maps of the anteroposterior prostate and nasopharynx IMRT fields were used as an input for the ANN (feed forward type), and a dose map of those fluence maps that were acquired by two-dimensional Array Seven29TM as an output for the ANN. RESULTS: After the training and validation of the neural network, the analysis of 20 IMRT anteroposterior fields showed excellent agreement between the ANN output and the dose map predicted by the treatment planning system. The average overall global and local γ field pass rate was greater than 90% for the prostate and nasopharynx fields, with the 2 mm/3% criteria. CONCLUSION: The results indicated that the ANN can be used as a fast and powerful tool for pretreatment dose verification, based on an EPID fluence map. ADVANCES IN KNOWLEDGE: In this study, ANN is proposed for EPID based dose validation of IMRT fields. The proposed method has good accuracy and high speed in response to problems. Neural network show to be low price and precise method for IMRT fields verification.

The Benefits of Decision Tree to Predict Survival in Patients with Glioblastoma Multiforme with the Use of Clinical and Imaging Features.

BACKGROUND: Machine learning is a type of artificial intelligence which aims to improve machine with the ability of extracting knowledge from the environment. Glioblastoma multiforme (GBM) is one of the most common and aggressive primary malignant brain tumors in adults. Due to a low rate of survival in patients with these tumors, machine learning can help physicians for better decision-making. The aim of this paper is to develop a machine learning model for predicting the survival rate of patients with GBM based on clinical features and magnetic resonance imaging (MRI). MATERIALS AND METHODS: The present investigation is an observational study conducted to predict the survival rate in patients with GBM in 12 months. Fifty-five patients who were registered in five Iranian Hospitals (Tehran) during 2012-2014 were selected in this study. RESULTS: This study used Cox and C5.0 decision tree models based on clinical features and combined them with MRI. Accuracy, sensitivity, and specification parameters used to evaluate the models. The result of Cox and C5.0 for clinical feature was <32.73%, 22.5%, 45.83%>, <72.73%, 67.74%, 79.19%>, respectively; also, the result of Cox and C5.0 for both features was <60%, 48.58%, 75%>, <90.91%, 96.77%, 88.33%>, respectively. CONCLUSION: Using C5.0 decision tree model in both survival models including clinical features, both the imaging features and the clinical features as the covariates, shows additional predictive values and better results. The tumor width and Karnofsky performance status scores were determined as the most important parameters in the survival prediction of these types of patients.

Assessment of the Agreement between Cerebral Hemodynamic Indices Quantified Using Dynamic Susceptibility Contrast and Dynamic Contrast-enhanced Perfusion Magnetic Resonance Imagings.

BACKGROUND: Brain tumor is one of the most common tumors. A successful treatment might be achieved with an early identification. Pathological investigation as the gold standard method for tumor identification has some limitations. Noninvasive assessment of tumor specifications may be possible using perfusion-weighted magnetic resonance imaging (MRI). Cerebral blood volume (CBV) and cerebral blood flow (CBF) could be calculated based on dynamic contrast-enhanced MRI (DCE-MRI) in addition to dynamic susceptibility contrast MRI (DSC-MRI) modality. Each category of the cerebral hemodynamic and permeability indices revealed the specific tumor characteristics and their collection could help for better identification of the tumor. Some mathematical methods were developed to determine both cerebral hemodynamic and permeability indices based on a single-dose DCE perfusion MRI. There are only a few studies available on the comparison of DSC- and DCE-derived cerebral hemodynamic indices such as CBF and CBV. AIM: The objective of the study was to validate first-pass perfusion parameters derived from T1-based DCE method in comparison to the routine T2*-based DSC protocol. MATERIALS AND METHODS: Twenty-nine patients with brain tumor underwent DCE- and DSC-MRIs to evaluate the agreement between DSC- and DCE-derived cerebral hemodynamic parameters. Agreement between DSC- and DCE-derived cerebral hemodynamic indices was determined using the statistical method described by Bland and Altman. The reliability between DSC- and DCE-derived cerebral hemodynamic indices was measured using the intraclass correlation analysis. RESULTS: The achieved magnitudes for DCE-derived CBV (gray matter [GM]: 5.01 ± 1.40 mL/100 g vs. white matter [WM]: 1.84 ± 0.74 mL/100 g) and DCE-derived CBF (GM: 60.53 ± 12.70 mL/100 g/min vs. WM: 32.00 ± 6.00 mL/100 g/min) were in good agreement with other studies. The intraclass correlation coefficients showed that the cerebral hemodynamic indices could accurately be estimated based on the DCE-MRI using a single-compartment model (>0.87), and DCE-derived cerebral hemodynamic indices are significantly similar to the magnitudes achieved based on the DSC-MRI (P < 0.001). Furthermore, an acceptable agreement was observed between DSC- and DCE-derived cerebral hemodynamic indices. CONCLUSION: Based on the measurement of the cerebral hemodynamic and blood-brain barrier permeability using DCE-MRI, a more comprehensive collection of the physiological parameters cloud be achieved for tumor evaluations.

The Role of Protein Kinase B Signaling Pathway in Anti-Cancer Effect of Rolipram on Glioblastoma Multiforme: An In Vitro Study.

INTRODUCTION: The mechanism of putative cytotoxicity of 4-[3-(cyclopentyloxy)-4-methoxyphenyl]-2-pyrrolidone (rolipram), a specific phosphodiesterase-4 (PDE4) inhibitor, on glioblastoma multiforme (GBM) is almost unknown. This study aimed to investigate the role of protein kinase B (Akt) pathway in the cytotoxic effect of rolipram on human GBM U87 MG cell line and Tumor-Initiating Cells (TICs) isolated from patient's GBM specimen. METHODS: TICs were characterized by using flow cytometry and quantitative real-time PCR. The cells were treated with rolipram at inhibitory concentration of 50% (IC50) in the presence or absence of SC79 (4µg/mL), a specific AKT activator, for 48 hours. The cell viability and apoptosis were measured by MTT assay and TUNEL staining, respectively. The relative expression of Phospho-Akt (Ser473), matrix metalloproteinase 2 (MMP2), and vascular endothelial growth factor A (VEGFA) were detected using Western blotting. RESULTS: The findings showed that rolipram could suppress cell viability in both U87MG and TICs, dose-dependently. Interestingly, the rolipram-induced cytotoxicity was significantly reduced in the presence of SC79. Nevertheless, in rolipram-treated cells, the pretreatment with SC79 significantly led to increase in U87 MG cells and TICs apoptosis and decrease in viability of U87 MG cells but not TICs relative to corresponding control. In U87 MG and TICs, rolipram-induced reduction of Phospho-Akt (Ser473) and MMP2 levels were significantly suppressed by SC79. CONCLUSION: There is a cell type-specific mechanism of anti-proliferative action of rolipram on GBM cells. The reduction of intracellular level of MMP2 but not VEGFA by rolipram is conducted through the inhibition of Akt signal. Rolipram-induced apoptosis is mediated via Akt dependent/independent mechanisms.

Association between promoter methylation and expression of thyroid hormone receptor beta (THRß) gene in patients with gastric cancer in an Iranian population.

BACKGROUND AND AIM: There is evidence that gastric cancer patients suffer from thyroid disorders. However, the relationship between thyroid receptor (TR) expression and gastric cancer remains unknown. The aim of this study was to evaluate the status of promoter methylation and expression of the thyroid hormone receptor beta (THRß) gene in gastric cancer patients in an Iranian population. METHODS: Analysis of THRß promoter methylation was performed on 85 pairs of formalin-fixed, paraffin-embedded (FFPE) tissue samples as cases and controls via methylation-specific polymerase chain reaction (PCR [MSP]). The samples were obtained from tumors and surrounding healthy tissues from resected gastric cancers. The expression assay was also performed with 25 FFPE tissue pairs (tumor and surrounding healthy tissues of the same individual) using real-time PCR. RESULTS: The results of the present study show that there is a statistically significant difference between tumor and adjacent normal tissues regarding promoter methylation status and THRß expression (P = 0.04 and P = 0.036, respectively). CONCLUSION: Therefore, promoter methylation of THRß may be involved in the development of gastric cancer.

hsa-mir-499 rs3746444 gene polymorphism is associated with susceptibility to breast cancer in an Iranian population.

AIM: Our study aimed to evaluate the possible association between four miRNA polymorphisms, hsa-miR-146a (rs2910164 G>C), hsa-miR-499 (rs3746444 T>C) and hsa-miRNA-196a2 (rs11614913 C>T and rs185070757 T>G), and susceptibility to breast cancer in an Iranian population. MATERIALS & METHODS: In this case-control study we enrolled 236 patients with breast cancer and 203 healthy individuals. Tetra primer amplification refractory mutation system PCR was applied for genotyping the four miRNA SNPs. RESULTS: Our study indicated that the hsa-mir-499 rs3746444 CC homozygote increased the risk of breast cancer in the dominant (odds ratio [OR]: 2.42; 95% CI: 1.43-4.09; p = 0.001; CC vs TT) and recessive (OR: 2.48; 95% CI: 1.49-4.13; p = 0.004; CC vs TT+TC) inheritance models tested. In addition, the rs3746444 C allele increased the risk of breast cancer (OR: 1.71; 95% CI: 1.27-2.29; p = 0.0004) in comparison with the T allele. However, distribution of the rs2910164 G>C, rs11614913 C>T and rs185070757 T>G genotypes was not statistically different between cases and controls (p > 0.05). CONCLUSION: Our findings demonstrated that the hsa-mir-499 rs3746444 polymorphism is associated with higher risk of developing breast cancer in our population.

Functional polymorphisms of FAS and FASL gene and risk of breast cancer - pilot study of 134 cases.

Fas/Fas ligand (FasL) system is one of the key apoptotic signaling entities in the extrinsic apoptotic pathway. De-regulation of this pathway, i.e. by mutations may prevent the immune system from the removal of newly-formed tumor cells, and thus lead to tumor formation. The present study investigated the association between -1377 G/A (rs2234767) and -670 A/G (rs1800682) polymorphisms in Fas as well as single nucleotide polymorphisms INV2nt -124 A/G (rs5030772) and -844 C/T (rs763110) in FasL in a sample of Iranian patients with breast cancer. This case-control study was done on 134 breast cancer patients and 152 normal women. Genomic DNA was extracted from whole blood samples. The polymorphisms were determined by using tetra-ARMS-PCR method. There was no significant difference in the genotype distribution of FAS rs2234767 polymorphism between cases and controls. FAS rs1800682, FASL rs5030772, and FASL rs763110 genotypes showed significant associations with an increasing risk of breast cancer (odds ratio OR = 3.18, P = 0.019; OR = 5.08, P = 0.012; OR = 2.40, P = 0.024, respectively). In conclusion, FAS rs2234767 was not associated with breast cancer risk. Though, FAS rs1800682, FASL rs5030772, and FASL rs763110 polymorphisms were associated with the risk of breast cancer in the examined population.

Association between polymorphisms of glutathione S-transferase genes (GSTM1, GSTP1 and GSTT1) and breast cancer risk in a sample Iranian population.

AIM: Genetic and environmental factors are risk factors for breast cancer. Our aim was to investigate the associations between genetic polymorphism of GST genes (GSTM1, GSTT1 and GSTP1) and susceptibility to breast cancer in an Iranian population. MATERIALS & METHODS: This case-control study was carried out on 134 patients with breast cancer and 152 healthy, cancer-free women. GSTP1 polymorphism was determined using tetra-primer amplification refractory mutation system PCR assay and GSTM1 and GSTT1 were genotyped by a multiplex PCR. RESULTS: We found that the GSTM1 null genotype is a risk factor for predisposition to breast cancer (odds ratio [OR] = 2.01; 95% CI = 1.78-3.45; p = 0.010). No significant difference was found between the groups regarding GSTT1 null genotype (p > 0.05). The GSTP1 Ile/Val and Val/Val genotypes were associated with breast cancer risk (OR = 3.29; 95% CI = 1.84-5.91; p < 0.0001 and OR = 20.68; 95% CI = 5.66-75.60; p < 0.0001, respectively). CONCLUSION: In summary, GSTM1 and GSTP1, but not GSTT1 genetic polymorphisms are associated with increased risk of breast cancer in our population.

Evaluation of UDP-glucuronosyltransferase 2B17 (UGT2B17) and dihydrofolate reductase (DHFR) genes deletion and the expression level of NGX6 mRNA in breast cancer.

The present study was aimed to investigate the possible association between 19-base pair (bp) deletion polymorphism of the DHFR gene (rs70991108), null genotype of UDP-glucuronosyltransferase 2B17 (UGT2B17) as well as the expression level of nasopharyngeal carcinoma-associated gene 6 (NGX6) with the risk of breast cancer. This case-control study was done on 236 patients with breast cancer and 203 cancer free women. Detection of 19-bp del of DHFR was done using bi-directional PCR allele-specific amplification and UGT2B17 genotyping was performed using multiplex PCR assay. NGX6 mRNA expression level was determined by quantitative reverse transcriptase PCR in 62 breast cancerous and 62 adjacent non-cancerous tissues. Our finding showed an association between null genotype of UGT2B17 and risk of breast cancer and the null genotype increased susceptibility to breast cancer (OR: 2.99; 95 % CI: 1.94-4.60; p < 0.0001). However, no statistically significant difference was found between breast cancer patients and cancer free normal women regarding 19-bp ins/del of DHFR (χ(2) = 0.91, p = 0.63). Real-time PCR data showed that the relative expression level of NGX6 mRNA was significantly lower in cancerous than that in non-cancerous breast tissue specimens (0.936 ± 0.042 and 1.042 ± 0.039, respectively). However, NGX6 mRNA expression was not correlated with tumors grade (p > 0.05). In conclusion, the null genotype of UGT2B17 revealed to be a risk factor for breast cancer in a sample of Iranian population. Furthermore, down-regulation of NGX6 mRNA expression in breast carcinoma confirms the growing proof regarding the tumor suppressor role of NGX6.

Bi-directional PCR allele-specific amplification (bi-PASA) for detection of caspase-8 -652 6N ins/del promoter polymorphism (rs3834129) in breast cancer.

Caspase-8 (CASP8) plays a critical role in regulating apoptosis, and its functional polymorphisms may modify cancer risk. We investigated the possible association between CASP8 -652 6N ins/del (rs3834129) and the risk of breast cancer in a sample of Iranian population. This case-control study was done on 236 breast cancer patients and 203 cancer free healthy female. We designed a rapid and simple bi-directional PCR allele-specific amplification (bi-PASA) for detection of CASP8 -652 6N ins/del polymorphism. The results showed that the CASP8 -652 6N del/dl genotype was inversely associated with breast cancer risk (OR=0.33, 95% CI=0.17-0.65, p=0.001). The frequencies of the del allele in cases and controls were 29.1% and 38.6%, respectively. An inverse association between CASP8 6N del variant and the risk of breast cancer (OR=0.66, 95% CI=0.66-0.87, p=0.002) was found. In conclusion, the result suggests that the CASP8 -652 6N del polymorphism plays a protective role in susceptibility to breast cancer in our population. Further studies in other populations with larger samples are needed to confirm these findings.

Genotyping of -374A/T, -429A/G, and 63 bp Ins/del polymorphisms of RAGE by rapid one-step hexaprimer amplification refractory mutation system polymerase chain reaction in breast cancer patients.

Several studies have focused on the RAGE genetic background and have demonstrated that its polymorphisms affect the receptor's activity, expression, and downstream signaling. However, there is only little information regarding RAGE polymorphism in breast cancer. In the present study, the authors studied RAGE polymorphisms in 71 patients with breast cancer and 93 healthy women. RAGE -374T/A, -429T/C, and 63 bp Ins/del polymorphisms were analyzed using a hexaprimer amplification refractory mutation system PCR (H-ARMS-PCR). The results showed that RAGE polymorphisms are not associated with breast cancer in the current study population. Larger studies are required to confirm these data in other populations.

A comprehensive test of clinical reasoning for medical students: An olympiad experience in Iran.

BACKGROUND: Although some tests for clinical reasoning assessment are now available, the theories of medical expertise have not played a major role in this filed. In this paper, illness script theory was chose as a theoretical framework and contemporary clinical reasoning tests were put together based on this theoretical model. MATERIALS AND METHODS: This paper is a qualitative study performed with an action research approach. This style of research is performed in a context where authorities focus on promoting their organizations' performance and is carried out in the form of teamwork called participatory research. RESULTS: Results are presented in four parts as basic concepts, clinical reasoning assessment, test framework, and scoring. CONCLUSION: we concluded that no single test could thoroughly assess clinical reasoning competency, and therefore a battery of clinical reasoning tests is needed. This battery should cover all three parts of clinical reasoning process: script activation, selection and verification. In addition, not only both analytical and non-analytical reasoning, but also both diagnostic and management reasoning should evenly take into consideration in this battery. This paper explains the process of designing and implementing the battery of clinical reasoning in the Olympiad for medical sciences students through an action research.